Buggy code:
@ Description ( "A<seq2seq4repair_space>multi-type<seq2seq4repair_space>phylogenetic<seq2seq4repair_space>tree." ) @ Citation ( "Timothy<seq2seq4repair_space>G.<seq2seq4repair_space>Vaughan,<seq2seq4repair_space>Denise<seq2seq4repair_space>Kuhnert,<seq2seq4repair_space>Alex<seq2seq4repair_space>Popinga,<seq2seq4repair_space>David<seq2seq4repair_space>Welch<seq2seq4repair_space>and<seq2seq4repair_space>\n" + ( "Alexei<seq2seq4repair_space>J.<seq2seq4repair_space>Drummond,<seq2seq4repair_space>\'Efficient<seq2seq4repair_space>Bayesian<seq2seq4repair_space>inference<seq2seq4repair_space>under<seq2seq4repair_space>the<seq2seq4repair_space>\n" + "structured<seq2seq4repair_space>coalescent',<seq2seq4repair_space>Bioinformatics<seq2seq4repair_space>30:2272,<seq2seq4repair_space>2014." ) ) public class MultiTypeTree extends Tree { public Input < String > typeLabelInput = new Input ( "typeLabel" , "Label<seq2seq4repair_space>for<seq2seq4repair_space>type<seq2seq4repair_space>traits<seq2seq4repair_space>(default<seq2seq4repair_space>'type')" , "type" ) ; public Input < TraitSet > typeTraitInput = new Input ( "typeTrait" , "Type<seq2seq4repair_space>trait<seq2seq4repair_space>set.<seq2seq4repair_space>Used<seq2seq4repair_space>only<seq2seq4repair_space>by<seq2seq4repair_space>BEAUti." ) ; public Input < List < String > > typeTraitValuesInput = new Input ( "typeTraitValue" , ( "An<seq2seq4repair_space>additional<seq2seq4repair_space>type<seq2seq4repair_space>value<seq2seq4repair_space>to<seq2seq4repair_space>be<seq2seq4repair_space>included<seq2seq4repair_space>even<seq2seq4repair_space>when<seq2seq4repair_space>absent<seq2seq4repair_space>" + "from<seq2seq4repair_space>the<seq2seq4repair_space>sampled<seq2seq4repair_space>taxa." ) , new ArrayList ( ) ) ; protected String typeLabel ; protected TraitSet typeTraitSet ; protected List < String > typeList ; public MultiTypeTree ( ) { } public MultiTypeTree ( Node rootNode ) { } @ Override public void initAndValidate ( ) throws Exception { } @ Override protected void processTraits ( List < TraitSet > traitList ) { } public TraitSet getTypeTrait ( ) { } public boolean hasTypeTrait ( ) { } public void setTypeTrait ( TraitSet traitSet ) { } public List < String > getTypeList ( ) { } public String getTypeString ( int type ) { } public int getTypeFromString ( String typeString ) { } public String getTypeLabel ( ) { } public int getNTypes ( ) { } @ Override protected final void initArrays ( ) { } private void listNodes ( MultiTypeNode node , MultiTypeNode [ ] nodes ) { } @ Override public MultiTypeTree copy ( ) { } @ Override public void assignFrom ( StateNode other ) { } @ Override public void assignFromFragile ( StateNode other ) { } private void assignFromFragileHelper ( int iStart , int iEnd , Node [ ] otherNodes ) { } public boolean isValid ( ) { } private boolean timesAreValid ( Node node ) { } private boolean typesAreValid ( Node node ) { } public Tree getFlattenedTree ( boolean useTypeStrings ) { } public void initFromFlatTree ( Tree flatTree , boolean takeNrsFromFlatTree ) throws Exception { } private int numberInternalNodes ( Node node , int nextNr ) { } public int getTotalNumberOfChanges ( ) { } @ Override public String toString ( ) { } @ Override protected void store ( ) { } private void storeNodes ( int iStart , int iEnd ) { } @ Override public void init ( PrintStream printStream ) throws Exception { } @ Override public void log ( int i , PrintStream printStream ) { } @ Override public void close ( PrintStream printStream ) { } @ Override public void fromXML ( org . w3c . dom . Node node ) { try { <START_BUG> String sNewick = node . getTextContent ( ) . replace ( "&" , "" ) ; <END_BUG> TreeParser parser = new TreeParser ( ) ; parser . initByName ( "IsLabelledNewick" , false , "offset" , 0 , "adjustTipHeights" , false , "singlechild" , true , "newick" , sNewick ) ; initFromFlatTree ( parser , true ) ; initArrays ( ) ; } catch ( Exception ex ) { Logger . getLogger ( MultiTypeTree . class . getName ( ) ) . log ( Level . SEVERE , null , ex ) ; } } }

Fix:
String sNewick = node . getTextContent ( ) ;